90 lines
3.3 KiB
Plaintext
90 lines
3.3 KiB
Plaintext
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R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences"
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Copyright (C) 2018 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> library(survival)
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> #
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> # A Cox model with a factor, followed by survexp.
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> #
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> pfit2 <- coxph(Surv(time, status > 0) ~ trt + log(bili) +
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+ log(protime) + age + platelet + sex, data = pbc)
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> esurv <- survexp(~ trt, ratetable = pfit2, data = pbc)
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>
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> temp <- pbc
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> temp$sex2 <- factor(as.numeric(pbc$sex), levels=2:0,
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+ labels=c("f", "m", "unknown"))
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> esurv2 <- survexp(~ trt, ratetable = pfit2, data = temp,
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+ rmap=list(sex=sex2))
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>
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> # The call components won't match, which happen to be first
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> all.equal(unclass(esurv)[-1], unclass(esurv2)[-1])
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[1] TRUE
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>
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>
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> # Check that the ratetableDate function is okay
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> #
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> Datedate <- function(x) {
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+ # Dates have an origin of 1/1/1970, dates of 1/1/1960
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+ offset <- as.numeric(as.Date("1970-01-01") - as.Date("1960-01-01"))
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+ y <- as.numeric(x) + offset
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+ class(y) <- "date"
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+ y
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+ }
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> as.data.frame.date <- as.data.frame.vector # needed to make the functions work
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>
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> n <- nrow(lung)
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> tdata <- data.frame(age=lung$age + (1:n)/365.25,
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+ sex = c('male', 'female')[lung$sex],
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+ ph.ecog = lung$ph.ecog,
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+ time = lung$time*3,
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+ status = lung$status,
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+ entry = as.Date("1940/01/01") + (n:1)*50)
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> tdata$entry2 <- as.POSIXct(tdata$entry)
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> tdata$entry3 <- Datedate(tdata$entry)
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>
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> p1 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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+ rmap= list(age=age*365.25, sex=sex, year=entry))
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> p2 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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+ rmap= list(age=age*365.25, sex=sex, year=entry2))
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> p3 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=survexp.us,
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+ rmap= list(age=age*365.25, sex=sex, year=entry3))
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>
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> all.equal(p1$expected, p2$expected)
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[1] TRUE
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> all.equal(p1$expected, p3$expected)
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[1] TRUE
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>
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>
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> # Now a ratetable with ordinary dates rather than US census style year
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> trate <- survexp.us
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> attr(trate, 'type') <- c(2,1,3)
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> p4 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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+ rmap= list(age=age*365.25, sex=sex, year=entry))
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> p5 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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+ rmap= list(age=age*365.25, sex=sex, year=entry2))
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> p6 <- pyears(Surv(time, status) ~ ph.ecog, data=tdata, ratetable=trate,
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+ rmap= list(age=age*365.25, sex=sex, year=entry3))
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>
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> #all.equal(p1$expected, p4$expected) # this won't be true, US special is special
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> all.equal(p4$expected, p5$expected)
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[1] TRUE
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> all.equal(p5$expected, p6$expected)
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[1] TRUE
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>
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> proc.time()
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user system elapsed
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0.756 0.036 0.790
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